See here is the thing, the fans are not giving him a hard time. (all my opinion this).
When your centre half is doing cruyff turns to the striker in his 6 yard box, of course the fans won't be happy with that. If the other lad had scored from it, it would hav been rightly classed as sunday league defending. So when the manager isn't coming out and basically calling him a tit for doing it and promising further coaching to help develop him then it raises issues.
Most fans know he isn't getting the support and development off the pitch, because none of them are. Considering his age, Stones should be getting every last bit of help on the training ground, but he clearly is just getting told to keep doing what he is doing, probably jags is his main trainer in that regard. Where MArtinez tells Barkely to just do his thing, its great because Ross can drive the ball forward, but elsewhere it doesn't work. When your centre half is messing about in his own box, or your young winger is just running into his man every time, then the coaching doesn't work.
So the overall point is, Stones is a victim of poor coaching, which translates into grumbles from the crowd when they can see that.